GitHub topics: trajectory-inference
jaydu1/VITAE
Joint Trajectory Inference for Single-cell Genomics Using Deep Learning with a Mixture Prior
Language: Jupyter Notebook - Size: 835 MB - Last synced at: 14 days ago - Pushed at: about 1 month ago - Stars: 27 - Forks: 8
CostaLab/phlower
Use hodge decomposition for trajectory analysis
Language: Python - Size: 34.8 MB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 4 - Forks: 0
MargaritaLiarou1/TimeFlow
TimeFlow: a density-driven pseudotime method for flow cytometry data analysis.
Language: Jupyter Notebook - Size: 38.8 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0
jr-leary7/scLANE
Characterize gene dynamics over trajectories using GLMs, GEEs, & GLMMs.
Language: R - Size: 31.3 MB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 10 - Forks: 3
dynverse/dynwrap
A common data format and inference environment for single-cell trajectories 📦
Language: R - Size: 15.4 MB - Last synced at: 16 days ago - Pushed at: almost 2 years ago - Stars: 16 - Forks: 5
renjun0324/ti_scfates_tree
A docker container for scFates, mainly for cell trajectory inference analysis of single cell RNA-seq data
Language: Python - Size: 34.2 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
renjun0324/MGPfact.jl
Trajectory inference method. It can decompose complex cell trajectories into interpretable transcriptional branching Gaussian processes.
Language: Julia - Size: 1.36 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0
renjun0324/MGPfactR
A model-based, unsupervised manifold learning method that factors complex cellular trajectories into interpretable bifurcating Gaussian processes of transcription.
Language: R - Size: 8.53 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0
xinglab-ai/genomap
Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data (Nature Communications, 2023)
Language: Python - Size: 43.7 MB - Last synced at: about 2 months ago - Pushed at: 11 months ago - Stars: 15 - Forks: 3
dynverse/dynguidelines
Selecting the optimal trajectory inference based on a given dataset and user input 🔮
Language: R - Size: 38 MB - Last synced at: 5 months ago - Pushed at: almost 5 years ago - Stars: 18 - Forks: 7
euxhenh/Truffle
Trajectory Inference of clinical data via Multi-commodity Flow
Language: Jupyter Notebook - Size: 99.6 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0
ShobiStassen/VIA
trajectory inference
Language: Jupyter Notebook - Size: 985 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 73 - Forks: 22
DaminK/GraphOTy
A Graph Optimal Transport Python Package
Language: Python - Size: 137 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 1 - Forks: 0
dynverse/dynbenchmark
Comparison of methods for trajectory inference on single-cell data 🥇
Language: R - Size: 20.8 MB - Last synced at: 12 months ago - Pushed at: over 1 year ago - Stars: 187 - Forks: 36
dynverse/dynmethods
A collection of 50+ trajectory inference methods within a common interface 📥📤
Language: R - Size: 18.9 MB - Last synced at: 12 months ago - Pushed at: over 1 year ago - Stars: 114 - Forks: 26
dynverse/dynplot
Visualising single-cell trajectories, including comparisons between two models 📈
Language: R - Size: 36.1 MB - Last synced at: 12 months ago - Pushed at: over 3 years ago - Stars: 29 - Forks: 5
Nuwa-genomics/Nuwa
A bioinformatics web app for single cell RNA seq analysis.
Language: Python - Size: 431 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
pientist/ballradar
[KDD 2023] Official implementation of "Ball Trajectory Inference from Multi-Agent Sports Contexts Using Set Transformer and Hierarchical Bi-LSTM".
Language: Jupyter Notebook - Size: 159 MB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 15 - Forks: 2
renjun0324/ti_mgpfact
The Docker container for MGPfact is primarily used for unsupervised manifold learning of single-cell RNA-seq data and can factorize complex cell trajectories into interpretable branching Gaussian processes.
Language: R - Size: 7.6 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
akds/Pseudocell-Tracer
Inferring cellular trajectories from scRNA-seq using Pseudocell Tracer
Language: Jupyter Notebook - Size: 73 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 5 - Forks: 0
dcellwanger/CellTrails
Mirror of the Bioconductor package CellTrails (http://bioconductor.org/packages/CellTrails/)
Language: R - Size: 41.8 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 3 - Forks: 2
dynverse/dyno
Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕
Language: R - Size: 114 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 149 - Forks: 32
aron0093/cytopath
Simulation based inference of differentiation trajectories from RNA velocity fields.
Language: Python - Size: 220 KB - Last synced at: 9 days ago - Pushed at: over 1 year ago - Stars: 10 - Forks: 4
StatBiomed/SingleCell-Workshop-2021
Module 4 for HKU Single-cell Workshop
Language: HTML - Size: 13.8 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 11 - Forks: 13
pdmoerland/SingleCellNotes
Links to interesting courses, tutorials, papers, software etc. related to single-cell omics data analysis
Size: 114 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 5 - Forks: 1
gaurav71531/fractDiffusion
Estimate space-time fractional diffusion equation from data
Language: Jupyter Notebook - Size: 264 KB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 0
zdong1/CDC
Swiss CDC Project Repository: Analyze and Predict human mobility patterns using kernel density ranking methods, and analyze the spatial-temporal trends of the activity spaces of human beings.
Language: R - Size: 253 KB - Last synced at: almost 2 years ago - Pushed at: almost 6 years ago - Stars: 4 - Forks: 0
